HEADER HYDROLASE 30-JAN-13 4IZS TITLE THE C145A MUTANT OF THE AMIDASE FROM NESTERENKONIA SP. AN1 IN COMPLEX TITLE 2 WITH BUTYRAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.1.4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NESTERENKONIA SP. 10004; SOURCE 3 ORGANISM_TAXID: 501897; SOURCE 4 STRAIN: AN1; SOURCE 5 GENE: NIT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BUTYRAMIDE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.W.KIMANI,B.T.SEWELL REVDAT 2 20-SEP-23 4IZS 1 REMARK SEQADV REVDAT 1 12-FEB-14 4IZS 0 JRNL AUTH S.W.KIMANI,R.HUNTER,M.VLOK,J.WATERMEYER,B.T.SEWELL JRNL TITL COVALENT MODIFICATIONS OF THE ACTIVE SITE CYSTEINE OCCUR AS JRNL TITL 2 A RESULT OF MUTATING THE GLUTAMATE OF THE CATALYTIC TRIAD IN JRNL TITL 3 THE AMIDASE FROM NESTERENKONIA SP. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 51256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2584 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3566 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.22000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -1.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.852 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2094 ; 0.033 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2868 ; 2.760 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 285 ; 6.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;36.766 ;24.316 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 318 ;12.371 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;23.261 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 319 ; 0.216 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1650 ; 0.017 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1338 ; 1.491 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2149 ; 2.474 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 756 ; 3.678 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 706 ; 6.043 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4IZS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000077415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51279 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 22.951 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : 0.38500 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: 3HKX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM, 2% PEG 400, 2.0 M REMARK 280 AMMONIUM SULFATE , PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.53000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.53000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.66000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.41500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.66000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.41500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.53000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.66000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.41500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.53000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.66000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.41500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 620 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 626 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 630 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 ASP A 238 REMARK 465 GLN A 239 REMARK 465 SER A 240 REMARK 465 GLN A 241 REMARK 465 ASP A 242 REMARK 465 ALA A 243 REMARK 465 GLY A 244 REMARK 465 SER A 245 REMARK 465 ASP A 246 REMARK 465 SER A 247 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A -3 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A -7 N GLY A -7 CA 0.110 REMARK 500 PRO A 86 N PRO A 86 CA 0.117 REMARK 500 GLU A 104 CG GLU A 104 CD -0.103 REMARK 500 GLU A 104 CD GLU A 104 OE1 0.098 REMARK 500 SER A 108 CB SER A 108 OG 0.085 REMARK 500 SER A 134 CA SER A 134 CB 0.092 REMARK 500 SER A 177 CB SER A 177 OG 0.102 REMARK 500 TYR A 196 CD1 TYR A 196 CE1 0.092 REMARK 500 VAL A 234 CB VAL A 234 CG2 -0.143 REMARK 500 GLU A 257 CG GLU A 257 CD 0.127 REMARK 500 ARG A 260 CZ ARG A 260 NH1 0.138 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 20 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 69 CG - CD - NE ANGL. DEV. = -15.4 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 75 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 100 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 GLU A 104 OE1 - CD - OE2 ANGL. DEV. = 8.9 DEGREES REMARK 500 LEU A 133 CB - CG - CD1 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 138 CG - CD - NE ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 138 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 160 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 160 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 249 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 249 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 TYR A 250 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 254 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 254 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 260 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 260 NE - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 145 -117.77 48.13 REMARK 500 ALA A 170 87.96 -154.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 69 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 91 -12.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMD A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HKX RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE WILD TYPE AMIDASE FROM NESTERENKONIA REMARK 900 AN1 SPECIES REMARK 900 RELATED ID: 4IZT RELATED DB: PDB REMARK 900 RELATED ID: 4IZU RELATED DB: PDB REMARK 900 RELATED ID: 4IZV RELATED DB: PDB REMARK 900 RELATED ID: 4IZW RELATED DB: PDB DBREF 4IZS A 1 263 UNP D0VWZ1 D0VWZ1_9MICC 1 263 SEQADV 4IZS MET A -19 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS GLY A -18 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS SER A -17 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS SER A -16 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -15 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -14 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -13 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -12 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -11 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A -10 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS SER A -9 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS SER A -8 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS GLY A -7 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS LEU A -6 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS VAL A -5 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS PRO A -4 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS ARG A -3 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS GLY A -2 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS SER A -1 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS HIS A 0 UNP D0VWZ1 EXPRESSION TAG SEQADV 4IZS ALA A 145 UNP D0VWZ1 CYS 145 ENGINEERED MUTATION SEQRES 1 A 283 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 283 LEU VAL PRO ARG GLY SER HIS MET ARG ILE ALA LEU MET SEQRES 3 A 283 GLN HIS THR ALA ARG PRO LEU ASP PRO GLN HIS ASN LEU SEQRES 4 A 283 ASP LEU ILE ASP ASP ALA ALA ALA ARG ALA SER GLU GLN SEQRES 5 A 283 GLY ALA GLN LEU LEU LEU THR PRO GLU LEU PHE GLY PHE SEQRES 6 A 283 GLY TYR VAL PRO SER GLN ILE CYS ALA GLN VAL SER ALA SEQRES 7 A 283 GLU GLN VAL ASP ALA ALA ARG SER ARG LEU ARG GLY ILE SEQRES 8 A 283 ALA ARG ASP ARG GLY ILE ALA LEU VAL TRP SER LEU PRO SEQRES 9 A 283 GLY PRO GLU GLY PRO GLU GLN ARG GLY ILE THR ALA GLU SEQRES 10 A 283 LEU ALA ASP GLU HIS GLY GLU VAL LEU ALA SER TYR GLN SEQRES 11 A 283 LYS VAL GLN LEU TYR GLY PRO GLU GLU LYS ALA ALA PHE SEQRES 12 A 283 VAL PRO GLY GLU GLN PRO PRO PRO VAL LEU SER TRP GLY SEQRES 13 A 283 GLY ARG GLN LEU SER LEU LEU VAL ALA TYR ASP VAL GLU SEQRES 14 A 283 PHE PRO GLU MET VAL ARG ALA ALA ALA ALA ARG GLY ALA SEQRES 15 A 283 GLN LEU VAL LEU VAL PRO THR ALA LEU ALA GLY ASP GLU SEQRES 16 A 283 THR SER VAL PRO GLY ILE LEU LEU PRO ALA ARG ALA VAL SEQRES 17 A 283 GLU ASN GLY ILE THR LEU ALA TYR ALA ASN HIS CYS GLY SEQRES 18 A 283 PRO GLU GLY GLY LEU VAL PHE ASP GLY GLY SER VAL VAL SEQRES 19 A 283 VAL GLY PRO ALA GLY GLN PRO LEU GLY GLU LEU GLY VAL SEQRES 20 A 283 GLU PRO GLY LEU LEU VAL VAL ASP LEU PRO ASP GLN SER SEQRES 21 A 283 GLN ASP ALA GLY SER ASP SER ALA ASP TYR LEU GLN ASP SEQRES 22 A 283 ARG ARG ALA GLU LEU HIS ARG ASN TRP LEU HET PEG A 301 7 HET PEG A 302 7 HET PEG A 303 7 HET BMD A 304 6 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM BMD BUTYRAMIDE FORMUL 2 PEG 3(C4 H10 O3) FORMUL 5 BMD C4 H9 N O FORMUL 6 HOH *230(H2 O) HELIX 1 1 ASP A 14 GLN A 32 1 19 HELIX 2 2 LEU A 42 GLY A 46 5 5 HELIX 3 3 VAL A 48 VAL A 56 1 9 HELIX 4 4 SER A 57 GLY A 76 1 20 HELIX 5 5 TYR A 115 PHE A 123 1 9 HELIX 6 6 VAL A 144 GLU A 149 5 6 HELIX 7 7 PHE A 150 ARG A 160 1 11 HELIX 8 8 THR A 176 ILE A 181 1 6 HELIX 9 9 ILE A 181 GLY A 191 1 11 HELIX 10 10 ASP A 249 ARG A 254 1 6 HELIX 11 11 ARG A 255 LEU A 263 1 9 SHEET 1 A 6 VAL A 105 GLN A 110 0 SHEET 2 A 6 THR A 95 ALA A 99 -1 N LEU A 98 O ALA A 107 SHEET 3 A 6 ALA A 78 TRP A 81 -1 N LEU A 79 O ALA A 99 SHEET 4 A 6 LEU A 36 LEU A 38 1 N LEU A 37 O VAL A 80 SHEET 5 A 6 MET A 1 GLN A 7 1 N MET A 6 O LEU A 38 SHEET 6 A 6 GLY A 230 LEU A 236 -1 O LEU A 236 N MET A 1 SHEET 1 B 6 VAL A 132 TRP A 135 0 SHEET 2 B 6 ARG A 138 LEU A 142 -1 O LEU A 140 N LEU A 133 SHEET 3 B 6 LEU A 164 PRO A 168 1 O LEU A 166 N SER A 141 SHEET 4 B 6 THR A 193 ALA A 197 1 O THR A 193 N VAL A 165 SHEET 5 B 6 VAL A 213 VAL A 215 -1 O VAL A 215 N LEU A 194 SHEET 6 B 6 PRO A 221 GLU A 224 -1 O LEU A 222 N VAL A 214 SHEET 1 C 2 CYS A 200 GLU A 203 0 SHEET 2 C 2 LEU A 206 ASP A 209 -1 O PHE A 208 N GLY A 201 SITE 1 AC1 5 ARG A 65 PRO A 86 GLU A 97 SER A 108 SITE 2 AC1 5 HOH A 405 SITE 1 AC2 7 GLN A 7 HIS A 8 ARG A 28 GLN A 91 SITE 2 AC2 7 GLY A 230 HOH A 495 HOH A 595 SITE 1 AC3 4 GLU A 118 ALA A 121 HOH A 512 HOH A 518 SITE 1 AC4 9 GLU A 41 TYR A 47 LYS A 111 TYR A 115 SITE 2 AC4 9 GLU A 119 ALA A 145 TYR A 146 GLU A 149 SITE 3 AC4 9 ALA A 170 CRYST1 75.320 114.830 65.060 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008709 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015370 0.00000